The main difference I saw was that Djokovic was able to go from defense to offense and back much more smoothly. He'd generally play conservatively but anytime he had an opening he'd go on the attack as evidenced by his gaudy winning % at the net. He was able to dictate play virtually every time when he faced a BP (admittedly not that many times but still some of these points were crucial)
Murray looked equally uncomfortable going fully on the offense or in extreme defense; on offense he would often stretch Joker to the extreme but he'd rarely pull the trigger for the killer shot. The lacking defense may have been because of the blisters but the refusal to go all out on the offense was mental, IMO.
Remember the great DTL backhand return winner he hit off one of Djok's serves? Did he ever try that one again??
Same with going to the net. He got passed once early in the match and then had several reasonably high-bouncing short balls where he'd run all the way forward, push the ball in the corner and then scamper back to the baseline. In similar circumstances Djokovic would hit an approach, go to the net and win the point.
Just the way I saw it, mind you